MolNFT v1 · #139527 · protein
Crystal structure of toxoplasma gondii prolyl-tRNA synthetase (tgprs) in complex with inhibitor 6
5XII · Prolyl-tRNA synthetase (prors): “Crystal structure of toxoplasma gondii prolyl-tRNA synthetase (tgprs) in complex with inhibitor 6”. X-ray diffraction, 4 ligands (ANP, 86X, MG), 19 pockets (best druggability 0.83). MolNFT v1 #139527…
- PDB
- 5XII
- Type
- protein
- Length
- 1,900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase (prors)
- EC
- 6.1.1.15
- UniProt
- S8G8I1
- Ligands
- ANP, 86X, MG, CL
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 476 | 37% helix, 29% strand | S8G8I1 |
| B | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 471 | 36% helix, 29% strand | S8G8I1 |
| C | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 479 | 37% helix, 29% strand | S8G8I1 |
| D | Prolyl-tRNA synthetase (prors) (EC 6.1.1.15) | protein | 474 | 38% helix, 29% strand | S8G8I1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- 86X · 6-chloranyl-7-fluoranyl-3-[3-[(2R)-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.83 | 0.87 | 74 | EDO |
| 2 | 942 | 0.82 | 0.84 | 90 | EDO, CL |
| 3 | 784 | 0.77 | 0.81 | 68 | ANP, MG, 86X |
| 4 | 682 | 0.76 | 0.81 | 60 | ANP, MG, 86X |
| 5 | 664 | 0.75 | 0.81 | 56 | ANP, MG, 86X |
Interfaces
4 interfaces between chains.
- B–D · 2717 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2610 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 339 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XII · Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt S8G8I1
- Elsewhere: RCSB PDB 5XII · PDBe 5XII · UniProt S8G8I1
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